Spinacia oleracea
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA286000 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2061370_1.fastq.gz | Fastqsanger.gz | |||
| SRR2061370_2.fastq.gz | Fastqsanger.gz | |||
| SRR2061692_1.fastq.gz | Fastqsanger.gz | |||
| SRR2061692_2.fastq.gz | Fastqsanger.gz | |||
| SRR2061413_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To examine the gene expression within the spinach root tissues as a response to exposure to nanoparticles. Methods: Sequenced reads were processed using CLC Genomics Workbench 7.0. The reads were trimmed based on quality, length and ambiguity. Resulting reads were assembled into transcript assemblies. Sequence reads were mapped back to the constructed transcriptome. TAs were BLAST searched against a local blast database of coding sequences of Arabidopsis thaliana. Statistical analysis was performed using Baggerley’s test. Transcript assemblies were tested for gene enrichment using GO annotations and the functional categories were determined. MapMan was used to visualize gene expression data of TAs and study the biological pathways. Results: De novo assembly of the trimmed reads yielded 147,733 Transcript Assemblies (TA) with an average length of 645 bp. Largest TA was 16,379 bp. Approximately 89% of the quality trimmed reads from the different samples mapped successfully to the assembly reference. Gene expression data for spinach TAs homologous to Arabidopsis genes show upregulation of protein degradation pathways in the nano-ZnO treatment compared to the non-nanoZnO, this upregulation is coupled with a down regulation of the genes in the protein synthesis pathways crucial role in the spinach plant responses to ZnO nanoparticle exposure. Genes associated (REDOX, signaling and transcription factors) with responses to stresses (both abiotic and biotic) were upregulated upon exposure to ZnO nanoparticles. Additionally genes in biosynthesis pathways of jasmonate and gibberellins genes were up-regulated upon exposure to ZnO nanoparticles in spinach. Conclusions: A de novo transcriptome was developed for spinach. When spinach plants were exposed to ZnO nanoparticles, they seem to sense the nanoparticles similarly to external chemicals or pathogens and induced production of reactive oxygen species. Hormone signaling pathways were activated leading to the induced expression of hormones with different roles in defense.
2018-09-10 | GSE72912 | GEO
Project description:Spinach (Spinacia oleracea L.) is an economically important and globally consumed popular leafy vegetable that is heat-sensitive. Heat stress caused by global climate change is one of the primary deleterious elements limiting spinach production worldwide. Little work has been done to explore the heat-responsive mechanisms of spinach under high temperature-induced stress. In the present study, we used iTRAQ-based proteomic and transcriptomic approaches to investigate physiological, metabolic, and proteomic responses of spinach in response to day / night temperature of 35°C / 25°C compared to 20°C / 15°C for 4 days. A total of 3,543 differentially expressed genes (DEGs) were detected using transcriptome sequencing, of which 2,086 DEGs were downregulated and 1,457 were upregulated. The DEGs were mainly involved in superoxide dismutase activity, catalase, and peroxidase activity. A total of 3,246 differentially abundant proteins were detected using iTAQ-based quantitative proteomic approach, from which 567 differentially expressed proteins (DEPs) (277 upregulated and 290 downregulated) were identified. DEPs were mainly assigned to pathways related to metabolism, signal transduction, protein degradation, defense, and antioxidant. Four genes - superoxide dismutase (SOD, LOC110788339), catalase (CAT, LOC110790286), peroxidase (POD, LOC110775253), and heat shock protein (HSP, LOC110799288) - were validated using quantitative real-time PCR (qRT-PCR) to verify the proteomic and transcriptomic analyses, showing different transcriptional and translational expression levels. The findings of this study provide a fundamental understanding of the metabolic pathways and biological processes that control adaptation to heat stress in spinach, and provide novel insight into the development of heat-tolerant spinach.
2020-06-24 | GSE153070 | GEO
Project description:Resequencing Data of spinach
| PRJNA608209 | ENA
Project description:Genome, Resequencing and Transcriptome data of Spinach
| PRJNA724923 | ENA
Project description:Zinc Oxide nanoparticles (ZnO NPs) are being rapidly developed for use in consumer products, wastewater treatment and chemotherapy providing several possible routes for ZnO NP exposure to humans and aquatic organisms. Recent studies have shown that ZnO NPs undergo rapid dissolution to Zn+2, but the relative contribution of Zn+2 to ZnO NP bioavailability and toxicity is not clear. Gene expression profiling of D. magna exposed to ZnO NPs or ZnSO4 at equitoxic concentrations demonstrated that the particles cause toxicity through a distinct mechanism compared with Zn+2. D. magna were also exposed to a SiO NPs as a particle control at equimolar concentrations. The SiO NPs resulted in few differentially expressed genes and there was very little overlap between the genes affected by the ZnO NPs and the SiO NPs, suggesting that ZnO NPs cause a distinct pattern of differentially expressed genes. In the ZnO NP exposures, effects were observed to genes involved in cytoskeletal transport, cellular respiration and reproduction. Three biomarker genes including a multi-cystatin, ferritin and a C1q containing gene were confirmed as differentially expressed in a specific pattern by ZnO NP and provide a suite of biomarkers for identifying environmental exposure to ZnO NP and differentiating between NP and ionic exposure. We exposed Daphnia magna to the 1/10 LC50 and LC25 of ZnO nanoparticles and Zn++ as ZnSO4 for 24-h. For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total). All exposures were compared to a unexposed laboratory control
2010-12-31 | E-GEOD-22051 | biostudies-arrayexpress
Project description:Transcriptome architecture reveals genetic networks of bolting regulation in spinach
| PRJNA630139 | ENA
Project description:Genome-wide association studies of Spinach for plant growth traits
| PRJNA779442 | ENA
Project description:Identification and expression profiling of flowering-related microRNAs in spinach
| PRJNA794004 | ENA
Project description:There is still a lot of contradiction on whether metal ions are solely responsible for the observed the toxicity of ZnO and CuO nanoparticles to aquatic species. While most tests have studied nanoparticle effects at organismal levels (e.g. mortality, reproduction), effects at suborganismal levels may clarify the role of metal ions, nanoparticles and nanoparticle aggregates. In this study, the effect of ZnO, CuO nanoparticles and zinc, copper salts was tested on the gene expression levels in Daphnia magna. D. magna was exposed during 96 hours to 10% immobilization concentrations of all chemicals, after which daphnids were sampled for a differential gene expression analysis using microarray. When comparing the nanoparticle exposed daphnids (ZnO or CuO) to the metal salt exposed daphnids (zinc or copper salt), the microarray results showed no significantly differentially expressed genes. These results indicate that the toxicity of the tested ZnO and CuO nanoparticles to D. magna caused is solely caused by toxic metal ions. 4 replicate exposures of ZnO nanoparticles, ZnCl2, Blank (for Zn); 4 replicate exposures of CuO nanoparticles, CuCl2.2H2O, Blank (for Cu); Individual reference design with swapped dyes for zinc (e.g. ZnO-REFZn; REFZn-bl) and copper exposure (e.g. CuO-REFCu; REFCu-bl); Zinc reference sample is a mixture of equal aliquots of ZnO nanoparticle, ZnCl2 and blank; Copper reference sample is a mixture of equal aliquots of CuO nanoparticle, CuCl2.2H2O and blank
2014-03-01 | E-GEOD-54738 | biostudies-arrayexpress
Project description:There is still a lot of contradiction on whether metal ions are solely responsible for the observed the toxicity of ZnO and CuO nanoparticles to aquatic species. While most tests have studied nanoparticle effects at organismal levels (e.g. mortality, reproduction), effects at suborganismal levels may clarify the role of metal ions, nanoparticles and nanoparticle aggregates. In this study, the effect of ZnO, CuO nanoparticles and zinc, copper salts was tested on the gene expression levels in Daphnia magna. D. magna was exposed during 96 hours to 10% immobilization concentrations of all chemicals, after which daphnids were sampled for a differential gene expression analysis using microarray. When comparing the nanoparticle exposed daphnids (ZnO or CuO) to the metal salt exposed daphnids (zinc or copper salt), the microarray results showed no significantly differentially expressed genes. These results indicate that the toxicity of the tested ZnO and CuO nanoparticles to D. magna caused is solely caused by toxic metal ions. 4 replicate exposures of ZnO nanoparticles, ZnCl2, Blank (for Zn); 4 replicate exposures of CuO nanoparticles, CuCl2.2H2O, Blank (for Cu); Individual reference design with swapped dyes for zinc (e.g. ZnO-REFZn; REFZn-bl) and copper exposure (e.g. CuO-REFCu; REFCu-bl); Zinc reference sample is a mixture of equal aliquots of ZnO nanoparticle, ZnCl2 and blank; Copper reference sample is a mixture of equal aliquots of CuO nanoparticle, CuCl2.2H2O and blank
2014-03-01 | E-GEOD-54736 | biostudies-arrayexpress